Job ID = 6367220 SRX = SRX3043406 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:01 prefetch.2.10.7: 1) Downloading 'SRR5875890'... 2020-06-15T23:17:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:12 prefetch.2.10.7: 'SRR5875890' is valid 2020-06-15T23:18:12 prefetch.2.10.7: 1) 'SRR5875890' was downloaded successfully Read 13123452 spots for SRR5875890/SRR5875890.sra Written 13123452 spots for SRR5875890/SRR5875890.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:49 13123452 reads; of these: 13123452 (100.00%) were unpaired; of these: 255074 (1.94%) aligned 0 times 10841012 (82.61%) aligned exactly 1 time 2027366 (15.45%) aligned >1 times 98.06% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1536130 / 12868378 = 0.1194 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:26:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:36: 1000000 INFO @ Tue, 16 Jun 2020 08:26:42: 2000000 INFO @ Tue, 16 Jun 2020 08:26:49: 3000000 INFO @ Tue, 16 Jun 2020 08:26:55: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:26:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:01: 5000000 INFO @ Tue, 16 Jun 2020 08:27:06: 1000000 INFO @ Tue, 16 Jun 2020 08:27:08: 6000000 INFO @ Tue, 16 Jun 2020 08:27:13: 2000000 INFO @ Tue, 16 Jun 2020 08:27:15: 7000000 INFO @ Tue, 16 Jun 2020 08:27:20: 3000000 INFO @ Tue, 16 Jun 2020 08:27:22: 8000000 INFO @ Tue, 16 Jun 2020 08:27:27: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:27:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:29: 9000000 INFO @ Tue, 16 Jun 2020 08:27:34: 5000000 INFO @ Tue, 16 Jun 2020 08:27:36: 10000000 INFO @ Tue, 16 Jun 2020 08:27:36: 1000000 INFO @ Tue, 16 Jun 2020 08:27:40: 6000000 INFO @ Tue, 16 Jun 2020 08:27:43: 11000000 INFO @ Tue, 16 Jun 2020 08:27:43: 2000000 INFO @ Tue, 16 Jun 2020 08:27:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:27:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:27:45: #1 total tags in treatment: 11332248 INFO @ Tue, 16 Jun 2020 08:27:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:27:45: #1 tags after filtering in treatment: 11332248 INFO @ Tue, 16 Jun 2020 08:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:46: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 08:27:46: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:46: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:27:46: #2 alternative fragment length(s) may be 0,15,50,442,504,554,571 bps INFO @ Tue, 16 Jun 2020 08:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:46: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:46: #2 You may need to consider one of the other alternative d(s): 0,15,50,442,504,554,571 WARNING @ Tue, 16 Jun 2020 08:27:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:27:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:47: 7000000 INFO @ Tue, 16 Jun 2020 08:27:50: 3000000 INFO @ Tue, 16 Jun 2020 08:27:54: 8000000 INFO @ Tue, 16 Jun 2020 08:27:57: 4000000 INFO @ Tue, 16 Jun 2020 08:28:01: 9000000 INFO @ Tue, 16 Jun 2020 08:28:04: 5000000 INFO @ Tue, 16 Jun 2020 08:28:08: 10000000 INFO @ Tue, 16 Jun 2020 08:28:11: 6000000 INFO @ Tue, 16 Jun 2020 08:28:15: 11000000 INFO @ Tue, 16 Jun 2020 08:28:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:17: #1 total tags in treatment: 11332248 INFO @ Tue, 16 Jun 2020 08:28:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:28:17: #1 tags after filtering in treatment: 11332248 INFO @ Tue, 16 Jun 2020 08:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:18: 7000000 INFO @ Tue, 16 Jun 2020 08:28:18: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 08:28:18: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:18: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:28:18: #2 alternative fragment length(s) may be 0,15,50,442,504,554,571 bps INFO @ Tue, 16 Jun 2020 08:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:18: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:18: #2 You may need to consider one of the other alternative d(s): 0,15,50,442,504,554,571 WARNING @ Tue, 16 Jun 2020 08:28:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:25: 8000000 INFO @ Tue, 16 Jun 2020 08:28:31: 9000000 INFO @ Tue, 16 Jun 2020 08:28:38: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:44: 11000000 INFO @ Tue, 16 Jun 2020 08:28:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:46: #1 total tags in treatment: 11332248 INFO @ Tue, 16 Jun 2020 08:28:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:28:47: #1 tags after filtering in treatment: 11332248 INFO @ Tue, 16 Jun 2020 08:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:47: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 08:28:47: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:48: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:28:48: #2 alternative fragment length(s) may be 0,15,50,442,504,554,571 bps INFO @ Tue, 16 Jun 2020 08:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043406/SRX3043406.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:48: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:48: #2 You may need to consider one of the other alternative d(s): 0,15,50,442,504,554,571 WARNING @ Tue, 16 Jun 2020 08:28:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at147/job_scripts/6367220: line 271: 5522 Terminated MACS $i /var/spool/uge/at147/job_scripts/6367220: line 271: 14656 Terminated MACS $i /var/spool/uge/at147/job_scripts/6367220: line 271: 15531 Terminated MACS $i ls: cannot access SRX3043406.05.bed: No such file or directory mv: cannot stat ‘SRX3043406.05.bed’: No such file or directory mv: cannot stat ‘SRX3043406.05.bb’: No such file or directory ls: cannot access SRX3043406.10.bed: No such file or directory mv: cannot stat ‘SRX3043406.10.bed’: No such file or directory mv: cannot stat ‘SRX3043406.10.bb’: No such file or directory ls: cannot access SRX3043406.20.bed: No such file or directory mv: cannot stat ‘SRX3043406.20.bed’: No such file or directory mv: cannot stat ‘SRX3043406.20.bb’: No such file or directory